A comparison of methods for classifying clinical samples based on proteomics data : a case study for statistical and machine learning approaches

The discovery of protein variation is an important strategy in disease diagnosis within the biological sciences. The current benchmark for elucidating information from multiple biological variables is the so called “omics” disciplines of the biological sciences. Such variability is uncovered by implementation of multivariable data mining techniques which come under two primary categories, machine learning strategies and statistical based approaches. Typically proteomic studies can produce hundreds or thousands of variables, p, per observation, n, depending on the analytical platform or method employed to generate the data. Many classification methods are limited by an n≪p constraint, and as such, require pre-treatment to reduce the dimensionality prior to classification. Recently machine learning techniques have gained popularity in the field for their ability to successfully classify unknown samples. One limitation of such methods is the lack of a functional model allowing meaningful interpretation of results in terms of the features used for classification. This is a problem that might be solved using a statistical model-based approach where not only is the importance of the individual protein explicit, they are combined into a readily interpretable classification rule without relying on a black box approach. Here we incorporate statistical dimension reduction techniques Partial Least Squares (PLS) and Principal Components Analysis (PCA) followed by both statistical and machine learning classification methods, and compared them to a popular machine learning technique, Support Vector Machines (SVM). Both PLS and SVM demonstrate strong utility for proteomic classification problems.

Representing USDL for humans and tools

This chapter deals with technical aspects of how USDL service descriptions can be read from and written to different representations for use by humans and tools. A combination of techniques for representing and exchanging USDL have been drawn from Model-Driven Engineering and Semantic Web technologies. The USDL language's structural definition is specified as a MOF meta-model, but some modules were originally defined using the OWL language from the Semantic Web community and translated to the meta-model format. We begin with the important topic of serializing USDL descriptions into XML, so that they can be exchanged beween editors, repositories, and other tools. The following topic is how USDL can be made available through the Semantic Web as a network of linked data, connected via URIs. Finally, consideration is given to human-readable representations of USDL descriptions, and how they can be generated, in large part, from the contents of a stored USDL model.

Sustainable Road Management in Texas : network-level flexible pavement structural condition analysis using data mining techniques

The research team recognized the value of network-level Falling Weight Deflectometer (FWD) testing to evaluate the structural condition trends of flexible pavements. However, practical limitations due to the cost of testing, traffic control and safety concerns and the ability to test a large network may discourage some agencies from conducting the network-level FWD testing. For this reason, the surrogate measure of the Structural Condition Index (SCI) is suggested for use. The main purpose of the research presented in this paper is to investigate data mining strategies and to develop a prediction method of the structural condition trends for network-level applications which does not require FWD testing. The research team first evaluated the existing and historical pavement condition, distress, ride, traffic and other data attributes in the Texas Department of Transportation (TxDOT) Pavement Maintenance Information System (PMIS), applied data mining strategies to the data, discovered useful patterns and knowledge for SCI value prediction, and finally provided a reasonable measure of pavement structural condition which is correlated to the SCI. To evaluate the performance of the developed prediction approach, a case study was conducted using the SCI data calculated from the FWD data collected on flexible pavements over a 5-year period (2005 – 09) from 354 PMIS sections representing 37 pavement sections on the Texas highway system. The preliminary study results showed that the proposed approach can be used as a supportive pavement structural index in the event when FWD deflection data is not available and help pavement managers identify the timing and appropriate treatment level of preventive maintenance activities.

Data analysis skills for teachers

Although accountability in the form of high stakes testing is in favour in the contemporary Australian educational context, this practice remains a highly contested source of debate. Proponents for high stakes tests claim that higher standards in teaching and learning result from their implementation, whereas others believe that this type of testing regime is not required and may even in fact be counterproductive. Regardless of what side of the debate you sit on, the reality is that at present, high stakes testing appears to be here to stay. It could therefore be argued it is essential that teachers understand accountability and possess the specific skills to interpret and use test data beneficially.

Joining the dots : piloting the work diary as a data collection tool for educational research

This paper demonstrates the affordances of the work diary as a data collection tool for both pilot studies and qualitative research of social interactions. Observation is the cornerstone of many qualitative, ethnographic research projects (Creswell, 2008). However, determining through observation, the activities of busy school teams could be likened to joining dots of a child’s drawing activity to reveal a complex picture of interactions. Teachers, leaders and support personnel are in different locations within a school, performing diverse tasks for a variety of outcomes, which hopefully achieve a common goal. As a researcher, the quest to observe these busy teams and their interactions with each other was daunting and perhaps unrealistic. The decision to use a diary as part of a wider research project was to overcome the physical impossibility of simultaneously observing multiple team members. One reported advantage of the use of the diary in research was its suitability as a substitute for lengthy researcher observation, because multiple data sets could be collected at once (Lewis et al, 2005; Marelli, 2007).

Stakeholders' perceptions of data utility in the context of ERP outcomes

A substantial body of literature exists identifying factors contributing to under-performing Enterprise Resource Planning systems (ERPs), including poor communication, lack of executive support and user dissatisfaction (Calisir et al., 2009). Of particular interest is Momoh et al.’s (2010) recent review identifying poor data quality (DQ) as one of nine critical factors associated with ERP failure. DQ is central to ERP operating processes, ERP facilitated decision-making and inter-organizational cooperation (Batini et al., 2009). Crucial in ERP contexts is that the integrated, automated, process driven nature of ERP data flows can amplify DQ issues, compounding minor errors as they flow through the system (Haug et al., 2009; Xu et al., 2002). However, the growing appreciation of the importance of DQ in determining ERP success lacks research addressing the relationship between stakeholders’ requirements and perceptions of ERP DQ, perceived data utility and the impact of users’ treatment of data on ERP outcomes.

Indications for early hip revision surgery in the UK : A re-analysis of NJR data

This study determined the rate and indication for revision between cemented, uncemented, hybrid and resurfacing groups from NJR (6 th edition) data. Data validity was determined by interrogating for episodes of misclassification. We identified 6,034 (2.7%) misclassified episodes, containing 97 (4.3%) revisions. Kaplan-Meier revision rates at 3 years were 0.9% cemented, 1.9% for uncemented, 1.2% for hybrids and 3.0% for resurfacings (significant difference across all groups, p<0.001, with identical pattern in patients <55 years). Regression analysis indicated both prosthesis group and age significantly influenced failure (p<0.001). Revision for pain, aseptic loosening, and malalignment were highest in uncemented and resurfacing arthroplasty. Revision for dislocation was highest in uncemented hips (significant difference between groups, p<0.001). Feedback to the NJR on data misclassification has been made for future analysis. © 2012 Wichtig Editore.

Population structure of Bactrocera dorsalis s.s., B. papayae and B. philippinensis (Diptera: Tephritidae) in southeast Asia: evidence for a single species hypothesis using mitochondrial DNA and wingshape data

Background Bactrocera dorsalis s.s. is a pestiferous tephritid fruit fly distributed from Pakistan to the Pacific, with the Thai/Malay peninsula its southern limit. Sister pest taxa, B. papayae and B. philippinensis, occur in the southeast Asian archipelago and the Philippines, respectively. The relationship among these species is unclear due to their high molecular and morphological similarity. This study analysed population structure of these three species within a southeast Asian biogeographical context to assess potential dispersal patterns and the validity of their current taxonomic status. Results Geometric morphometric results generated from 15 landmarks for wings of 169 flies revealed significant differences in wing shape between almost all sites following canonical variate analysis. For the combined data set there was a greater isolation-by-distance (IBD) effect under a ‘non-Euclidean’ scenario which used geographical distances within a biogeographical ‘Sundaland context’ (r2 = 0.772, P < 0.0001) as compared to a ‘Euclidean’ scenario for which direct geographic distances between sample sites was used (r2 = 0.217, P < 0.01). COI sequence data were obtained for 156 individuals and yielded 83 unique haplotypes with no correlation to current taxonomic designations via a minimum spanning network. BEAST analysis provided a root age and location of 540kya in northern Thailand, with migration of B. dorsalis s.l. into Malaysia 470kya and Sumatra 270kya. Two migration events into the Philippines are inferred. Sequence data revealed a weak but significant IBD effect under the ‘non-Euclidean’ scenario (r2 = 0.110, P < 0.05), with no historical migration evident between Taiwan and the Philippines. Results are consistent with those expected at the intra-specific level. Conclusions Bactrocera dorsalis s.s., B. papayae and B. philippinensis likely represent one species structured around the South China Sea, having migrated from northern Thailand into the southeast Asian archipelago and across into the Philippines. No migration is apparent between the Philippines and Taiwan. This information has implications for quarantine, trade and pest management.

Fusing loop detector and probe vehicle data to estimate travel time statistics on signalized urban networks

This article presents a methodology that integrates cumulative plots with probe vehicle data for estimation of travel time statistics (average, quartile) on urban networks. The integration reduces relative deviation among the cumulative plots so that the classical analytical procedure of defining the area between the plots as the total travel time can be applied. For quartile estimation, a slicing technique is proposed. The methodology is validated with real data from Lucerne, Switzerland and it is concluded that the travel time estimates from the proposed methodology are statistically equivalent to the observed values.

Analysis of acoustic emission data for accurate damage assessment for structural health monitoring applications

Structural health monitoring (SHM) refers to the procedure used to assess the condition of structures so that their performance can be monitored and any damage can be detected early. Early detection of damage and appropriate retrofitting will aid in preventing failure of the structure and save money spent on maintenance or replacement and ensure the structure operates safely and efficiently during its whole intended life. Though visual inspection and other techniques such as vibration based ones are available for SHM of structures such as bridges, the use of acoustic emission (AE) technique is an attractive option and is increasing in use. AE waves are high frequency stress waves generated by rapid release of energy from localised sources within a material, such as crack initiation and growth. AE technique involves recording these waves by means of sensors attached on the surface and then analysing the signals to extract information about the nature of the source. High sensitivity to crack growth, ability to locate source, passive nature (no need to supply energy from outside, but energy from damage source itself is utilised) and possibility to perform real time monitoring (detecting crack as it occurs or grows) are some of the attractive features of AE technique. In spite of these advantages, challenges still exist in using AE technique for monitoring applications, especially in the area of analysis of recorded AE data, as large volumes of data are usually generated during monitoring. The need for effective data analysis can be linked with three main aims of monitoring: (a) accurately locating the source of damage; (b) identifying and discriminating signals from different sources of acoustic emission and (c) quantifying the level of damage of AE source for severity assessment. In AE technique, the location of the emission source is usually calculated using the times of arrival and velocities of the AE signals recorded by a number of sensors. But complications arise as AE waves can travel in a structure in a number of different modes that have different velocities and frequencies. Hence, to accurately locate a source it is necessary to identify the modes recorded by the sensors. This study has proposed and tested the use of time-frequency analysis tools such as short time Fourier transform to identify the modes and the use of the velocities of these modes to achieve very accurate results. Further, this study has explored the possibility of reducing the number of sensors needed for data capture by using the velocities of modes captured by a single sensor for source localization. A major problem in practical use of AE technique is the presence of sources of AE other than crack related, such as rubbing and impacts between different components of a structure. These spurious AE signals often mask the signals from the crack activity; hence discrimination of signals to identify the sources is very important. This work developed a model that uses different signal processing tools such as cross-correlation, magnitude squared coherence and energy distribution in different frequency bands as well as modal analysis (comparing amplitudes of identified modes) for accurately differentiating signals from different simulated AE sources. Quantification tools to assess the severity of the damage sources are highly desirable in practical applications. Though different damage quantification methods have been proposed in AE technique, not all have achieved universal approval or have been approved as suitable for all situations. The b-value analysis, which involves the study of distribution of amplitudes of AE signals, and its modified form (known as improved b-value analysis), was investigated for suitability for damage quantification purposes in ductile materials such as steel. This was found to give encouraging results for analysis of data from laboratory, thereby extending the possibility of its use for real life structures. By addressing these primary issues, it is believed that this thesis has helped improve the effectiveness of AE technique for structural health monitoring of civil infrastructures such as bridges.

Application of an appearance-based intervention to improve sun protection outcomes of outdoor workers in Queensland, Australia

Outdoor workers are exposed to high levels of ultraviolet radiation (UVR) and may thus be at greater risk to experience UVR-related health effects such as skin cancer, sun burn, and cataracts. A number of intervention trials (n=14) have aimed to improve outdoor workers’ work-related sun protection cognitions and behaviours. Only one study however has reported the use of UV-photography as part of a multi-component intervention. This study was performed in the USA and showed long-term (12 months) improvements in work-related sun protection behaviours. Intervention effects of the other studies have varied greatly, depending on the population studied, intervention applied, and measurement of effect. Previous studies have not assessed whether: - Interventions are similarly effective for workers in stringent and less stringent policy organisations; - Policy effect is translated into workers’ leisure time protection; - Implemented interventions are effective in the long-term; - The facial UV-photograph technique is effective in Australian male outdoor workers without a large additional intervention package, and; - Such interventions will also affect workers’ leisure time sun-related cognitions and behaviours. Therefore, the present Protection of Outdoor Workers from Environmental Radiation [POWER]-study aimed to fill these gaps and had the objectives of: a) assessing outdoor workers’ sun-related cognitions and behaviours at work and during leisure time in stringent and less stringent sun protection policy environments; b) assessing the effect of an appearance-based intervention on workers’ risk perceptions, intentions and behaviours over time; c) assessing whether the intervention was equally effective within the two policy settings; and d) assessing the immediate post-intervention effect. Effectiveness was described in terms of changes in sun-related risk perceptions and intentions (as these factors were shown to be main precursors of behaviour change in many health promotion theories) and behaviour. The study purposefully selected and recruited two organisations with a large outdoor worker contingent in Queensland, Australia within a 40 kilometre radius of Brisbane. The two organisations differed in the stringency of implementation and reinforcement of their organisational sun protection policy. Data were collected from 154 male predominantly Australian born outdoor workers with an average age of 37 years and predominantly medium to fair skin (83%). Sun-related cognitions and behaviours of workers were assessed using self-report questionnaires at baseline and six to twelve months later. Variation in follow-up time was due to a time difference in the recruitment of the two organisations. Participants within each organisation were assigned to an intervention or control group. The intervention group participants received a one-off personalised Skin Cancer Risk Assessment Tool [SCRAT]-letter and a facial UV-photograph with detailed verbal information. This was followed by an immediate post-intervention questionnaire within three months of the start of the study. The control group only received the baseline and follow-up questionnaire. Data were analysed using a variety of techniques including: descriptive analyses, parametric and non-parametric tests, and generalised estimating equations. A 15% proportional difference observed was deemed of clinical significance, with the addition of reported statistical significance (p<0.05) where applicable. Objective 1: Assess and compare the current sun-related risk perceptions, intentions, behaviours, and policy awareness of outdoor workers in stringent and less stringent sun protection policy settings. Workers within the two organisations (stringent n=89 and less stringent n=65) were similar in their knowledge about skin cancer, self efficacy, attitudes, and social norms regarding sun protection at work and during leisure time. Participants were predominantly in favour of sun protection. Results highlighted that compared to workers in a less stringent policy organisation working for an organisation with stringent sun protection policies and practices resulted in more desirable sun protection intentions (less willing to tan p=0.03) ; actual behaviours at work (sufficient use of upper and lower body protection, headgear, and sunglasses (p<0.001 for all comparisons), and greater policy awareness (awareness of repercussions if Personal Protective Equipment (PPE) was not used, p<0.001)). However the effect of the work-related sun protection policy was found not to extend to leisure time sun protection. Objective 2: Compare changes in sun-related risk perceptions, intentions, and behaviours between the intervention and control group. The effect of the intervention was minimal and mainly resulted in a clinically significant reduction in work-related self-perceived risk of developing skin cancer in the intervention compared to the control group (16% and 32% for intervention and control group, respectively estimated their risk higher compared to other outdoor workers: , p=0.11). No other clinical significant effects were observed at 12 months follow-up. Objective 3: Assess whether the intervention was equally effective in the stringent sun protection policy organisation and the less stringent sun protection policy organisation. The appearance-based intervention resulted in a clinically significant improvement in the stringent policy intervention group participants’ intention to protect from the sun at work (workplace*time interaction, p=0.01). In addition to a reduction in their willingness to tan both at work (will tan at baseline: 17% and 61%, p=0.06, at follow-up: 54% and 33%, p=0.07, stringent and less stringent policy intervention group respectively. The workplace*time interaction was significant p<0.001) and during leisure time (will tan at baseline: 42% and 78%, p=0.01, at follow-up: 50% and 63%, p=0.43, stringent and less stringent policy intervention group respectively. The workplace*time interaction was significant p=0.01) over the course of the study compared to the less stringent policy intervention group. However, no changes in actual sun protection behaviours were found. Objective 4: Examine the effect of the intervention on level of alarm and concern regarding the health of the skin as well as sun protection behaviours in both organisations. The immediate post-intervention results showed that the stringent policy organisation participants indicated to be less alarmed (p=0.04) and concerned (p<0.01) about the health of their skin and less likely to show the facial UV-photograph to others (family p=0.03) compared to the less stringent policy participants. A clinically significantly larger proportion of participants from the stringent policy organisation reported they worried more about skin cancer (65%) and skin freckling (43%) compared to those in the less stringent policy organisation (46%,and 23% respectively , after seeing the UV-photograph). In summary the results of this study suggest that the having a stringent work-related sun protection policy was significantly related to for work-time sun protection practices, but did not extend to leisure time sun protection. This could reflect the insufficient level of sun protection found in the general Australian population during leisure time. Alternatively, reactance caused by being restricted in personal decisions through work-time policy could have contributed to lower leisure time sun protection. Finally, other factors could have also contributed to the less than optimal leisure time sun protection behaviours reported, such as unmeasured personal or cultural barriers. All these factors combined may have lead to reduced willingness to take proper preventive action during leisure time exposure. The intervention did not result in any measurable difference between the intervention and control groups in sun protection behaviours in this population, potentially due to the long lag time between the implementation of the intervention and assessment at 12-months follow-up. In addition, high levels of sun protection behaviours were found at baseline (ceiling effect) which left little room for improvement. Further, this study did not assess sunscreen use, which was the predominant behaviour assessed in previous effective appearance-based interventions trials. Additionally, previous trials were mainly conducted in female populations, whilst the POWER-study’s population was all male. The observed immediate post-intervention result could be due to more emphasis being placed on sun protection and risks related to sun exposure in the stringent policy organisation. Therefore participants from the stringent policy organisation could have been more aware of harmful effects of UVR and hence, by knowing that they usually protect adequately, not be as alarmed or concerned as the participants from the less stringent policy organisation. In conclusion, a facial UV-photograph and SCRAT-letter information alone may not achieve large changes in sun-related cognitions and behaviour, especially of assessed 6-12 months after the intervention was implemented and in workers who are already quite well protected. Differences found between workers in the present study appear to be more attributable to organisational policy. However, against a background of organisational policy, this intervention may be a useful addition to sun-related workplace health and safety programs. The study findings have been interpreted while respecting a number of limitations. These have included non-random allocation of participants due to pre-organised allocation of participants to study group in one organisation and difficulty in separating participants from either study group. Due to the transient nature of the outdoor worker population, only 105 of 154 workers available at baseline could be reached for follow-up. (attrition rate=32%). In addition the discrepancy in the time to follow-up assessment between the two organisations was a limitation of the current study. Given the caveats of this research, the following recommendations were made for future research: - Consensus should be reached to define "outdoor worker" in terms of time spent outside at work as well as in the way sun protection behaviours are measured and reported. - Future studies should implement and assess the value of the facial UV-photographs in a wide range of outdoor worker organisations and countries. - More timely and frequent follow-up assessments should be implemented in intervention studies to determine the intervention effect and to identify the best timing of booster sessions to optimise results. - Future research should continue to aim to target outdoor workers’ leisure time cognitions and behaviours and improve these if possible. Overall, policy appears to be an important factor in workers’ compliance with work-time use of sun protection. Given the evidence generated by this research, organisations employing outdoor workers should consider stringent implementation and reinforcement of a sun protection policy. Finally, more research is needed to improve ways to generate desirable behaviour in this population during leisure time.

Analysing seasonal data

Many common diseases, such as the flu and cardiovascular disease, increase markedly in winter and dip in summer. These seasonal patterns have been part of life for millennia and were first noted in ancient Greece by both Hippocrates and Herodotus. Recent interest has focused on climate change, and the concern that seasons will become more extreme with harsher winter and summer weather. We describe a set of R functions designed to model seasonal patterns in disease. We illustrate some simple descriptive and graphical methods, a more complex method that is able to model non-stationary patterns, and the case–crossover for controlling for seasonal confounding.

Sharing environmental data : the role of an information policy framework and copyright licensing

Advances in information and communication technologies have brought about an information revolution, leading to fundamental changes in the way that information is collected or generated, shared and distributed. The importance of establishing systems in which research findings can be readily made available to and used by other researchers has long been recognized in international scientific collaborations. If the data access principles adopted by international scientific collaborations are to be effectively implemented they must be supported by the national policies and laws in place in the countries in which participating researchers are operating.

Researcher attitudes to data sharing : cultural change requires better motivations

While undertaking the ANDS RDA Gold Standard Record Exemplars project, research data sharing was discussed with many QUT researchers. Our experiences provided rich insight into researcher attitudes towards their data and the sharing of such data. Generally, we found traditional altruistic motivations for research data sharing did not inspire researchers, but an explanation of the more achievement-oriented benefits were more compelling.